Acute allograft glomerulopathy (AAG) is a distinct form of allograft rejection characterized by cytotoxic T-cell-mediated injury to the renal glomerular and arteriolar endothelium. Acute allograft glomerulopathy is characterized by mononuclear cell infiltration of glomerular capillary tufts in association with endothelial cell hypertrophy and injury. Intra-glomerular thrombi have been described in AAG, suggesting that overlapping features of AAG and post-transplant thrombotic microangiopathy (TMA) may coexist. We present a case suggesting that complement factor H deficiency, a known hereditary risk factor for TMA, may also favor development of AAG. We discuss the potential implications of factor H deficiency in the pathophysiology of renal allograft microvascular injury, leukocyte infiltration and formation of intraglomerular platelet thrombi. We propose that unopposed complement activation is a risk factor for both immune and nonimmune forms of microvascular injuries in renal allografts.